When you look into SYSD (system.c) you'll see that DR1000 does various things before turning off. Most importantly, it unmounts the volume (/media/mmcblk0p1). This triggers running applications to commit changes and close their files. Doing this before calling shutdown will probably make it safer.

Yeah, that's what I suspected. I figured there were probably additional things done other than init stopping running processes before the device is safely shutdown. I would assume that the current script I have is killing the applications first, and then unmounting the volume.

I'll look into SYSD some more. This was just such a tempting shortcut though, that I couldn't resist trying it to see what would happen. Oh well.